You would need to re-align the Pano in your normal software and then upload the new image and swap the old/new images over by Editing the old Pano in 360Cities , select the Other tab and go to the bottom of the page where the option too swap images is available.

There are quite a few Tutorials on the PTGui site, also a lot of FAQ's that cover very specific problems that people meet. Also take a look at John Houghton's Tutorials and of course the support site for PTGui here on Google groups.

In PTGui use vertical or horizontal control points to make a perfect alignment. In the "Control points" tab select the same picture and look for vertical or horizontal objects in your pano. Something that you know for sure is in one of this two situation. (light poles, doors, buildings etc...) Optimize and you're done!